Do we know for sure if they're shooting with 3D cameras or doing it in post? If the latter, then the extra time would only be used to set up the 3D shots that show off the extra dimension.

Yes they are shooting in native 3D. Something the BBC have done a grand total of once before with a drama. (And had to compromise by keeping the shots relatively simple in order to get it done in time.)

In general you want much simpler and steadier camerawork with slow and deliberate editing when you're shooting in 3d. I haven't seen what it is you're referring to but don't mistake such things as (necessarily)trade-offs when they are quite intentional in order to get the most out of the medium.

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"There is no reason why good cannot triumph as often as evil. The triumph of anything is a matter of organization. If there are such things as angels, I hope that they are organized along the lines of the Maffia." - Winston Niles Rumfoord.